Here are some of the doctrinal issues:
Infant baptism
baptismal regeneration
ordination of women
ordination of practicing homosexuals
artificial birth control
sola scriptura
sola fide
The Rapture
From a governance perspective, did Jesus establish leadership within the one Church beginning with Peter and the Apostles followed by their successors the bishops? If so, then every non-Catholic group which is not in full communion with the Bishop of Rome is a separate and distinct group with its own man-made leadership.
To add to this list, there are many differences with regards to salvation such as how God saves his people and ‘election,’ for example, the reformed (Calvinist) people believe that God predestines people from the beginning as either among the elect or among the damned and chooses their fate according to his perfect will. Others believe that God granted us free will to choose or reject him (this is closer to what the Catholic Church believes).
Dispensationalists have different opinions regarding how God relates to the human race throughout history, and it’s a point that many Protestants disagree pretty strongly on. Also dispensationalists have a heavy focus on eschatology and believe in the rapture. You would think that this wouldn’t be a big deal but to a lot of people it is.
Pentecostals have different believes about how the Holy Spirit manifests itself among the Church. I can’t detail too much on this as I don’t remember much of what Pentecostals believe about this. I do know that they put a lot of emphasis on speaking in tongues and “charismatic-ness.” I remember my RCIA instructor telling a story about a pentecostal woman who visited our parish for mass and saying that she thought everyone looked so “spiritually dead” because it was so solemn. I have been to a Pentecostal church once and I just remember people running up and down the isles, convulsing, jumping up and down, screaming at the top of their lungs, and generally acting like chimpanzees in a zoo.
More recently there have been developments where some churches are moving away from the doctrine of the trinity (for example, the oneness pentecostals, also perhaps the Jehovah’s witnesses) because they claim that the doctrine lacks biblical evidence, and are convinced that it was a Catholic invention.
There are tons of little splinter groups who have various beliefs that they hold to be extremely important and upon which they separate themselves from other believers.
As a whole evangelicalism is constantly trying to reinvent itself, especially the so-called “non-denominational” crowd. They particularly obsess over terms, for example, many evangelicals now refuse to call themselves Christian and instead refer to themselves as “followers of Jesus” or something more euphemistic, and they despise words like “religion” and tout the phrase “it’s not religion, it’s a relationship” and “I’m not religious, I love Jesus” and “Jesus came to abolish religion.” I remember hearing this in college and thinking this was some ploy to make Christianity sound “hip” and “cool” and appeal to the increasingly secular student population in order to draw them in; the problem is that nobody gets fooled by this. Redefining terms in order to trick people into becoming Christians without knowing it is not an effective means of evangelization. I think this approach to Christianity also makes the ground they are standing on extremely unstable, this is why they are abandoning so much with regard to morality and doctrine.